Re: [gmx-users] using g_angle

2012-03-01 Thread francesca vitalini
Hi all! I have a question about how g_angle works. Form what I understood from the manual, if I provide an index file with dihedral quadruplets, then g_angle with the options -ov -all and -type dihedral should give me a list of dihedral values one for each quadruplet. However when I do that I

[gmx-users] using g_angle

2012-02-29 Thread francesca vitalini
Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [ dihedrals ] 2 5 9 10 10 15 18 19 . However it produces a .xvg file where it gives me for each angle in degrees its probability. However, what I want is

Re: [gmx-users] using g_angle

2012-02-29 Thread Mark Abraham
On 29/02/2012 9:39 PM, francesca vitalini wrote: Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [ dihedrals ] 2 5 9 10 10 15 18 19 . mk_angndx might have helped. However it produces a .xvg file

Re: [gmx-users] using g_angle

2012-02-29 Thread francesca vitalini
2012/2/29 Mark Abraham mark.abra...@anu.edu.au: On 29/02/2012 9:39 PM, francesca vitalini wrote: Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [ dihedrals ] 2 5 9 10 10 15 18 19 . mk_angndx

Re: [gmx-users] using g_angle

2012-02-29 Thread Vedat Durmaz
hi francesca, i think what you are looking for is this g_sgangle $indexFile -f $traj -s $tpr -oa $outfile before that, you have to define two planes (by 3 atom indices each) in your index file [ dihed1 ] 523 680 3482 [ dihed2 ] 680 3482 3691 which you choose when having started

Re: [gmx-users] using g_angle

2012-02-29 Thread Mark Abraham
On 29/02/2012 11:54 PM, francesca vitalini wrote: 2012/2/29 Mark Abrahammark.abra...@anu.edu.au: On 29/02/2012 9:39 PM, francesca vitalini wrote: Hi all, I'm trying to use g_angle to calculate a list of dihedrals that I have into an hand made index file (angles.ndx), which looks like [

Re: [gmx-users] using g_angle

2012-02-29 Thread francesca vitalini
Hi Mark, Thanks for your answer. What I'm trying to do is calculate the value in degrees of the angles listed in my index file. If my index file looks like [ dihedral 1 ] 2 7 9 10 [ dihedral 2 ] 10 16 18 19 then if I use the command line g_angle -f aa.gro -s aa.tpr -n angles_prova.ndx -ov

Re: [gmx-users] using g_angle

2012-02-29 Thread Mark Abraham
On 1/03/2012 1:00 AM, francesca vitalini wrote: Hi Mark, Thanks for your answer. What I'm trying to do is calculate the value in degrees of the angles listed in my index file. If my index file looks like [ dihedral 1 ] 2 7 9 10 [ dihedral 2 ] 10 16 18 19 I said in my last email that my

Re: [gmx-users] using g_angle

2012-02-29 Thread francesca vitalini
Thank you. It worked now. Best Francesca 2012/2/29 Mark Abraham mark.abra...@anu.edu.au: On 1/03/2012 1:00 AM, francesca vitalini wrote: Hi Mark, Thanks for your answer. What I'm trying to do is calculate the value in degrees of  the angles listed in my index file. If my index file looks